PROC QTL
Pub-Date: Sep 15, 2009
Introduction:
PROC QTL is a user defined SAS procedure for mapping quantitative trait loci (QTL). The program was coded in C++ and the interface with the SAS system was conducted using the SAS/Toolkit software (citation). Since this procedure is not a built-in SAS procedure, users need to obtain a copy of the executable file of PROC QTL and install the software in their personal computers before PROC QTL can be executed. Of course, users need a regular SAS license prior to the installation of PROC QTL. Once PROC QTL is installed, users can call the procedure just like they call any other regular SAS procedures without noticing the differences between this customized procedure and other built-in SAS procedures.
Updates in Version 1.5.1:
Updates in Version 1.5:
EM Lasso
Pub-Date: Oct 26, 2009
Introduction:
There are four SAS programs, three data files and one Readme file. The data are stored in excel spread sheets in comma delimited format.
Manual: doc
Download: zip
QTL-Power
Pub-Date: Feb, 2008
Introduction:
This program is designed to calculate the statistical power for QTL detection using flanking markers for the following types of population, F2, BC, DH and RIL. The program can also calculate the sample size, the marker density, the Type I error and the size of QTL (expressed as proportion of the phenotypic variance explained by the QTL. There are a total of six parameters required for the program: type of population (PopType), Type I error (alpha), sample size (n), size of marker interval (d), and proportion of the phenotypic variance explained by the QTL (h2). The QTL of interest is always assumed to be in the middle of the marker interval, i.e., 0.5d cM away from either marker.
The program can calculate five of the six parameters (excluding population type) given the values of the remaining parameters. Users should provide the input values for the input paramaters and set missing value for the output parameter. The current setting of the program (after the proc iml statement) is to calculate the power for an F2 population given alpha=0.01, n=100, d=10 and h2=0.05. Users can modify the current setting to calculate the parameter of their own interest.
Download: .sas, .zip, .rar, .7z
QTL-by-SAS/SIBPAIR
Pub-Date: Jun, 2004
Introduction:
This is a unified SAS program for single marker analysis and interval mapping of QTL using the extended sib-pair method under the random model methodology.
The SAS macro language is used to implement the mixed model QTL mapping procedure. The program consists of four macros. The first macro qtlibd calculates the proportion of genes IBD shared by sibs at putative QTL positions along each chromosome. This macro handles missing and partially informative markers using the multipoint method. The second macro qtlscan (including qtlscan1 for use of an optimization subroutine of PROC IML and qtlscan2 for use of PROC MIXED) provides estimates of QTL variance components and the likelihood ratio test statistic for any putative positions of the genome. The third macro qtlcritic determines the critical value used to declare statistical significance using the approximate method of Piepho. The last macro qtlplot draws SAS graphs showing the test statistical profiles of the genome.
Shrinkage Mapping
Pub-Date: Nov, 2006
Introduction:
This program performs QTL mapping using hierarchical Bayesian models. It handles three types of experimental populations: backcross, F2, and four-way cross. The trait value can be either continuous or categorical, however, the program does not deal with multiple traits. The program supports both the Windows and the Unix.
Manual: .pdf
E-Bayes QTL
Pub-Date: Sep, 2006
Introduction:
In the Supplementary Material, we provide two data sets and three SAS programs. The two datasets include a simulated one and a real one (barley), both of which were analyzed and reported in the paper. The three SAS programs are EBAYES, SSVS and PENAL. Each of the SAS programs has been customized to run the simulated dataset without making any modification other than to specify the correct directory to store your input and output files. To analyze the barley data or your own data, slight modification of the programs is required. The necessary modification can be found in the comments of each program code.
Manual: .pdf
BMM Differential Analysis
Pub-Date: May, 2003
Introduction:
This program contains a set of SAS macros for QTL interval mapping and composite interval mapping in line crosses by the maximum likelihood method implemented via the EM algorithm.
Manual: .pdf
QTL-by-SAS 1.0
Pub-Date: Nov, 2002
Introduction:
This program contains a set of SAS macros for QTL interval mapping and composite interval mapping in line crosses by the maximum likelihood method implemented via the EM algorithm.